SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information
SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information
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DOI：
10.1111/j.1096-0031.2010.00329.x
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发表时间：
2011-04-01
期刊：
影响因子：
3.6
通讯作者：
Meier, Rudolf
中科院分区：
文献类型：
--
作者：
Vaidya, Gaurav;Lohman, David J.;Meier, Rudolf
我们提出了sequencemmatrix软件，旨在促进多基因数据集的组装和分析。通过拖放FASTA、NEXUS或TNT文件并将序列对齐到程序窗口中来连接基因。一个多基因数据集被连接并显示在电子表格中；每个序列由一个单元表示，该单元提供有关序列长度、索引数、不明确碱基（“n”）的数量和密码子信息的可用性的信息。或者，可以显示和导出序列的GenBank编号。具有数百个基因和分类群的矩阵可以在几分钟内连接起来，并以TNT， NEXUS或phillip格式导出，保留TNT和NEXUS文件的字符集和密码子信息。SequenceMatrix还创建分类单元集，列出分类单元具有最少数量的字符或基因片段，这有助于评估初步数据集。特定基因和物种的整个分类群、整个基因片段或单个序列可以排除出口。数据矩阵可以重新分割成其组成基因，基因片段可以导出为单个基因文件。SequenceMatrix还包括两个工具，可以帮助识别可能因实验室污染或数据管理错误而受损的序列。一种工具列出基因内相同或接近相同的序列，而另一种工具将一个基因的成对距离模式与所有剩余基因的组合模式进行比较。SequenceMatrix基于java，兼容Microsoft Windows、Apple MacOS X和Linux操作系统。该软件可从http://code.google.com/p/sequencematrix/.（C免费获得）Willi henning Society 2010。
We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/.(C) The Willi Hennig Society 2010.